Dataset: ProteOMZ Protein Level Spectral Counts
Deployment: FK160115

Total spectral count of proteins from R/V Falkor cruise 160115 for the ProteOMZ expedition in the Central Pacific in 2016.

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/737620

Principal Investigator:

Mak A. Saito (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Hannah Ake (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

The ProteOMZ Expedition: Investigating Life Without Oxygen in the Pacific Ocean (ProteOMZ (Proteomics in an Oxygen Minimum Zone))

Current State:

Final no updates expected

Version:

Deployment Synonyms:

ProteOMZ

Version Date:

2018-05-25

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Description

These data are part of the Ocean Protein Portal "ProteOMZ" dataset (https://proteinportal.whoi.edu/; Saito et al., 2019).

Methods & Sampling

Dataset acquisition description

Data Processing Description

Dataset Processing Description

The raw mass spectra files were searched against SEQUEST within Proteome Discoverer v2.2 software. Processed files were then loaded into Proteome Software and protein and peptide reports as well as and fasta files were exported. The files were modified slightly to map to the Protein Portal data model for submission to BCO-DMO.

More information about this dataset deployment

Funding

Award Number	Funding Source
GBMF3782	Gordon and Betty Moore Foundation: Marine Microbiology Initiative
R/V Falkor 160115 SOI ProteOMZ Expedition	Schmidt Ocean Institute

Instruments

Alpkem RFA300

Supplied Name: Alpkem Autosampler

Supplied Description:

Used in nutrient analysis

Instrument Type

Generic Name: Alpkem RFA300

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0414/

Generic Description:

A rapid flow analyser (RFA) that may be used to measure nutrient concentrations in seawater. It is an air-segmented, continuous flow instrument comprising a sampler, a peristaltic pump which simultaneously pumps samples, reagents and air bubbles through the system, analytical cartridge, heating bath, colorimeter, data station, and printer. The RFA-300 was a precursor to the smaller Alpkem RFA/2 (also RFA II or RFA-2).

CTD Sea-Bird

Supplied Name: SeaBird SBE19 CTD

Supplied Description:

Used for water sampling

Instrument Type

Generic Name: CTD Sea-Bird

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics, no specific unit identified. This instrument designation is used when specific make and model are not known. See also other SeaBird instruments listed under CTD. More information from Sea-Bird Electronics.

Technicon AutoAnalyzer II

Supplied Description:

Used to measure phosphate and ammonium

Instrument Type

Generic Name: Technicon AutoAnalyzer II

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0291/

Generic Description:

A rapid flow analyzer that may be used to measure nutrient concentrations in seawater. It is a continuous segmented flow instrument consisting of a sampler, peristaltic pump, analytical cartridge, heating bath, and colorimeter. See more information about this instrument from the manufacturer.

Trace Metal Bottle

Supplied Name: Trace Metal Rosette

Supplied Description:

Used for nutrient sampling

Instrument Type

Generic Name: Trace Metal Bottle

Acronym: TM Bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/30/

Generic Description:

Trace metal (TM) clean rosette bottle used for collecting trace metal clean seawater samples.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_id	Unique sample name for the specific filter collected (station/depth/version if applicable)	untiless	sample
MS_MS_sample_name	Unique name for the mass spec sample and run	untiless	no_bcodmo_term
station_id	The identifier for the station	unitless	station
depth_m	Cast depth where sample was taken	meters	depth
latitude_dd	Latitude of station	decimal degrees	lat
longitude_dd	Longitude of station	decimal degrees	lon
date_ymd	Date of sampling (local time zone HST)	unitless	date
time_hms	Time of sampling (local time zone HST)	unitless	time
minimum_filter_size_microns	Minimum size of the collection filter	microns	filter_size
maximum_filter_size_microns	Maximum size of the collection filter	microns	filter_size
cruise_id	The unique cruise identifier	unitless	cruise_id
protein_id	The specific name of the full protein length sequence assembled in the metagenome that was used for peptide identification. An identifier that uniquely identifies this protein within this dataset and the FASTA file (see Related Datasets).	unitless	protein_ID
spectral_count_sum	Spectral count of each protein	count	spectral_counts
molecular_weight_kDa	Molecular weight of the full length protein sequences	kDa	weight
protein_name	Descriptive name of the function of the protein	unitless	accession_number
ncbi_id	NCBI Taxonomy organism identifier (for ncbi_name)	taxon	species
ncbi_name	NCBI Taxonomy name (corresponding to ncbi_id)	verbatimIdentifiation	taxon
kegg_id	The Kegg Orthology Entry identifier for the best Kegg match.	unitless	accession_number
kegg_description	Description of the function of the specific KEGG protein group	unitless	no_bcodmo_term
kegg_pathway	Decription of the cellular pathway that the KEGG protein is a part of.	unitless	no_bcodmo_term
pfams_id	Protein family (Pfam) ID number	unitless	accession_number
pfams_name	Protein family (Pfam) description	unitless	no_bcodmo_term
uniprot_id	Uniprot database ID number	unitless	accession_number
enzyme_comm_id	Enzyme Commission ID number	unitless	accession_number
ISO_DateTime_UTC	Datetime with timezone (UTC) of sampling in ISO 8601 format	unitless	ISO_DateTime_UTC

Database

Contribute Data

Dataset: ProteOMZ Protein Level Spectral Counts
Deployment: FK160115

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: ProteOMZ Protein Level Spectral CountsDeployment: FK160115

Dataset acquisition description

Dataset Processing Description

Dataset: ProteOMZ Protein Level Spectral Counts
Deployment: FK160115